1DFF

PEPTIDE DEFORMYLASE

Summary for 1DFF

• Entry DOI: 10.2210/pdb1dff/pdb
• Descriptor: PEPTIDE DEFORMYLASE, ZINC ION (3 entities in total)
• Functional Keywords: hydrolase, zinc metalloprotease
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 18863.13

Authors

Chan, M.K.,Gong, W.,Rajagopalan, P.T.R.,Hao, B.,Tsai, C.M.,Pei, D. (deposition date: 1997-08-19, release date: 1998-09-02, Last modification date: 2024-02-07)

Primary citation

Chan, M.K.,Gong, W.,Rajagopalan, P.T.,Hao, B.,Tsai, C.M.,Pei, D.
Crystal structure of the Escherichia coli peptide deformylase.
Biochemistry, 36:13904-13909, 1997

PubMed Abstract: Protein synthesis in bacteria involves the formylation and deformylation of the N-terminal methionine. As eukaryotic organisms differ in their protein biosynthetic mechanisms, peptide deformylase, the bacterial enzyme responsible for deformylation, represents a potential target for antibiotic studies. Here we report the crystallization and 2.9 A X-ray structure solution of the zinc containing Escherichia coli peptide deformylase. While the primary sequence, tertiary structure, and use of coordinated cysteine suggest that E. coli deformylase belongs to a new subfamily of metalloproteases, the environment around the metal appears to have strong geometric similarity to the active sites of the thermolysin family. This suggests a possible similarity in their hydrolytic mechanisms. Another important issue is the origin of the enzyme's specificity for N-formylated over N-acetylated substrates. Based on the structure, the specificity appears to result from hydrogen-bonding interactions which orient the substrate for cleavage, and steric factors which physically limit the size of the N-terminal carbonyl group.

PubMed: 9374869
DOI: 10.1021/bi9711543

Experimental method

X-RAY DIFFRACTION (2.88 Å)